I have a couple here that have lasted years, now, with no ill effect to them.The sides/edges of these TRCs weren't all that smooth to begin with, and they don't appear to be any worse than (old) factory stock ones that I have (mid 1960s- mid 1970s), with the WO on them.
Either one can work, and one is not necessarily safer than the other. Here is the deal on Plexiglas and other acrylics: When you work them (cut, sand, drill, etc.) it builds up internal stress inside the plastic. This makes it more prone to cracking or shattering without much provocation and sometimes from just coming into contact with solvents like cleaners and paint. In a perfect world, after working it, the plexi is annealed in an oven (heated to a low temperature like 200 degrees F for an hour or so and then allowed to cool slowly). This de-stresses it and makes it less prone to damage at cut edges, at screw holes, or from solvents. If you ever do something like making your own pick guards, it is well worth sticking them on a cookie sheet in the oven once the machining is done and annealing them before painting.
Are TRCs annealed at the factory before painting? I don't know, but kind of doubt it. One thing that can help is the old factory trick of sticking a small hunk of masking tape on the back of a TRC or pickguard at each screw hole. It both adds a little bit of cushion at the hole to help prevent the plexi from cracking and also reduces paint being pulled off of the plexi parts. Your TRC already has those little spider cracks around the holes, so it would be a very good idea. Also be careful not to overtighten the screws to prevent cracking.
As for the edges, if you really want nice ones you can do it by hand wet sanding in about 20 minutes with around three bucks worth of various grits of wet or dry sandpaper. Add a little rubbing compound and you can have perfect polished edges.
Whatever you do, be sure to put some masking tape on the back (once it's good and dry) so the truss rod nuts don't damage it again! For the sides, consider taking all the paint off... looks really cool.
Given the option, I'd probably go with acrylic enamel, like automobile touch-up paint or the water-based acrylics made for painting models. Most regular spray paint will also work and have pretty mild solvents (like mineral spirits) though I would avoid those containing more aggressive solvents - toluene, acetone, lacquer thinner, etc. If in doubt, put or spray a small blob on scrap, pick up a little bit on a toothpick and transfer it to a small test spot on the TRC to see if it dries OK and doesn't attack the old paint.
I mention just out of curiosity that I've seen water-based acrylic spray paints at the hardware store. Perhaps this would be a option if solvents are a concern?